: I think there's a great amount of evidence that: 1) Something happened to
: Cortana inside the Core (onset of Rampancy). This explains here initial
: rush of euphoria when connected to it, and her feeling of being
: "cooped up" after some time. She "expanded" while in
: the Core. (How we're able to fit her back inside the MC's cranium is
: another question.)

: 2) This change is not entirely positive. Cortana acts and appears more
: aggressive as a result. And she does appear to deceive Foe Hammer.

: However, becoming a bad AI isn't the same thing as being
: "convicted"-- this implies judgment, not commission. There's
: been no one to pass judgment on Cortana in that time, in fact, no one is
: aware of what else she might have done in that time. So the word
: "convict" does not seem to apply.

: Moreover, "escape" denotes imprisonment. One might assume this
: meant Cortana's containment in the Core, but it seems more likely this
: refers to the Flood. They are being held on an installation designed to
: study them that has a device designed to destroy all life in the galaxy to
: prevent even the possibility of their escape-- a device the MC and Cortana
: have now destroyed.

: To assume that Cortana and the MC know better than the Forerunners how to
: combat the Flood seems arrogant pride; and as we all know, pride goeth
: before a fall.

: To me, it seems more likely that, as at the end of "Aliens", some
: Flood have escaped on the Longsword with us. They are the
: "convicts"-- they were convicted by the Forerunners of the
: heinous crime of being unable to play well with others.

: GS would be the only one capable of considering Cortana a
: "convict"-- but this seems a stretch. "Conviction"
: implies authority, and there's no reason that the MC, Cortana, or anyone
: else in the game universe would consider his judgment authoritative.

So then something else was imprisoned in the Core. This could explain why 343GS was so upset with a construct in the core. Because it was being used as prison for another AI. Cortana accidently released the imprisoned AI. The new AI infiltrated Cortana and is hitch a ride with her.